1BOWTIE2-BUILD(1)                 User Commands                BOWTIE2-BUILD(1)
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NAME

6       bowtie2-build - manual page for bowtie2-build 2.4.1
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SYNOPSIS

9       bowtie2-build [options]* <reference_in> <bt2_index_base>
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DESCRIPTION

12       Bowtie   2   version   2.4.1   by   Ben  Langmead  (langmea@cs.jhu.edu,
13       www.cs.jhu.edu/~langmea)
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15       reference_in
16              comma-separated list of files with ref sequences
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18       bt2_index_base
19              write bt2 data to files with this dir/basename
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21       *** Bowtie 2 indexes work only with v2 (not v1).  Likewise for  v1  in‐
22       dexes. *** Options:
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24       -f     reference files are Fasta (default)
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26       -c     reference sequences given on cmd line (as <reference_in>)
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28       --large-index
29              force  generated index to be 'large', even if ref has fewer than
30              4 billion nucleotides
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32       --debug
33              use the debug binary; slower, assertions enabled
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35       --sanitized
36              use sanitized binary; slower, uses ASan and/or UBSan
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38       --verbose
39              log the issued command
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41       -a/--noauto
42              disable automatic -p/--bmax/--dcv memory-fitting
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44       -p/--packed
45              use packed strings internally; slower, less memory
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47       --bmax <int>
48              max bucket sz for blockwise suffix-array builder
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50       --bmaxdivn <int>
51              max bucket sz as divisor of ref len (default: 4)
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53       --dcv <int>
54              diff-cover period for blockwise (default: 1024)
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56       --nodc disable diff-cover (algorithm becomes quadratic)
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58       -r/--noref
59              don't build .3/.4 index files
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61       -3/--justref
62              just build .3/.4 index files
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64       -o/--offrate <int>
65              SA is sampled every 2^<int> BWT chars (default: 5)
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67       -t/--ftabchars <int>
68              # of chars consumed in initial lookup (default: 10)
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70       --threads <int>
71              # of threads
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73       --seed <int>
74              seed for random number generator
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76       -q/--quiet
77              verbose output (for debugging)
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79       -h/--help
80              print detailed description of tool and its options
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82       --usage
83              print this usage message
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85       --version
86              print version information and quit
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90bowtie2-build 2.4.1              January 2022                 BOWTIE2-BUILD(1)
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